pathseq-build-microbe-reference.inputs.json

{
  "##_COMMENT1": "References and Resources",
  "PathSeqBuildMicrobeReferenceWorkflow.microbe_fasta": "gs://gatk-best-practices/pathseq/resources/meats.fa",
  "#PathSeqBuildMicrobeReferenceWorkflow.BuildPathSeqTaxonomyFile.catalog_file": "String (optional, default = \"catalog.gz\")",
  "#PathSeqBuildMicrobeReferenceWorkflow.BuildPathSeqTaxonomyFile.taxdump_file": "String (optional, default = \"taxdump.tar.gz\")",

  "##_COMMENT2": "Workflow Options",
  "#PathSeqBuildMicrobeReferenceWorkflow.min_non_virus_contig_length": "Int? (optional)",

  "##_COMMENT3": "Docker",
  "PathSeqBuildMicrobeReferenceWorkflow.gatk_docker": "broadinstitute/gatk:4.0.11.0",
  "#PathSeqBuildMicrobeReferenceWorkflow.gatk4_jar_override": "File? (optional)",

  "##_COMMENT4": "Runtime Parameter",
  "#PathSeqBuildMicrobeReferenceWorkflow.index_fasta_mem_gb": "Int? (optional)",
  "#PathSeqBuildMicrobeReferenceWorkflow.index_fasta_disk_gb": "Int? (optional)",
  "#PathSeqBuildMicrobeReferenceWorkflow.bwa_mem_index_mem_gb": "Int? (optional)",
  "#PathSeqBuildMicrobeReferenceWorkflow.bwa_mem_index_disk_gb": "Int? (optional)",
  "#PathSeqBuildMicrobeReferenceWorkflow.build_taxonomy_mem_gb": "Int? (optional)",
  "#PathSeqBuildMicrobeReferenceWorkflow.build_taxonomy_disk_gb": "Int? (optional)",
  "#PathSeqBuildMicrobeReferenceWorkflow.preemptible_attempts": "Int? (optional)"
}